Number of OTUs in all my samples

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#1

Hi All,

I just want to know how to make a simple table with the number of OTU associated with each sample. Currently there is a qiime diversity core-metrics-phylogenetic but it requires that I choose a sampling depth. How can I view the number of OTUs in all my samples without choosing a sampling depth? This would be similar to the summarize function in Qiime 1.

Thanks in advance

#2

Good afternoon,

How about this script?
https://docs.qiime2.org/2017.11/plugins/available/feature-table/summarize/

You can also return diversity metrics without rarefying / choosing a sampling depth by using this script:
https://docs.qiime2.org/2017.11/plugins/available/diversity/alpha/

Let me know if those help!
Colin

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#3

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